Swanson Hydrology & Geomorphology

115 Limekiln Street Santa Cruz, California USA 95060

phone 831-427-0288 / fax 427-0472 / email: swanson@swansonh2o.com

Hydrologic Issues regarding Management of

Pescadero Marsh in light of Enhancement
Projects completed in 1993 and 1997
A report to California Department of Parks and Recreation

Submitted 12/15/2000
Revised 10/29/2001

Introduction

This paper describes hydrologic, ecological and land use issues surrounding the
management of the Pescadero Marsh Natural Preserve by California Department of Parks
and Recreation. The primary purpose is to update marsh conditions after the
implementation of the 1990 Hydrologic Enhancement Plan (prepared by John Williams,
PhD. of Philip Williams & Associates Ltd., 1990) and to provide direction for CDPR to
address key environmental issues including management of newly listed endangered
species and conflicts with surrounding landowners regarding drainage issues.

Pescadero Marsh is a 340-acre Natural Preserve managed by the California Department

of Parks and Recreation. The marsh is an estuary through which the watersheds of
Pescadero Creek and Butano Creek drain. It is a complex of fresh, salt and brackish
marshes with two stream/riparian corridors and surrounding upland areas. Rural and
agricultural lands bound it to the north, east, and south, and the Highway 1 Corridor and
coastal zone to the west. The marsh was subject to agricultural reclamation for
agricultural in the early 1900s, and many of the marsh areas are surrounded and
hydrologicaly controlled by levees; this has significantly modified the hydrology of the
marsh. The "unnatural" levee system has apparently enhanced conditions for two
endangered species, the California Red legged frog and the San Francisco Garter Snake
(Reis and Smith, 1997). These and many other wildlife species are found in Pescadero
Marsh making it one of the richest ecosystems on the central California coast.

The focus of this report is to assess the effects of enhancement projects constructed in
1993 and 1997. This was accomplished through a review of the 1990 Enhancement Plan,
biotic reports made subsequent to the enhancement work, a review of memos and
miscellaneous reports generated by CDPR, numerous visits to the Marsh, and discussions
with CDPR personnel, local residents and those who have conducted research in the
Marsh. A hydraulic study of the Pescadero Creek Road Bridge over Butano Creek,

Hydrology / Geomorphology / Restoration / Water Resources / Construction Planning

& Supervision
 Swanson Hydrology & Geomorphology
Page 2
completed in 1999 by Swanson Hydrology and Geomorphology for the County of San
Mateo, was also incorporated.

Implemented Portions of the 1990 Pescadero Marsh Hydrological Enhancement

Plan

The goal of the 1990 enhancement plan was to restore the apparent hydrologic conditions
reflected on early maps (1853) and aerial photographs (1920s). The primary method was
to strategically remove reclamation levees and restore tidal prism and circulation to
marsh areas. The plan was partially implemented in early 1993 and additional work was
done in 1997.

Below is an abbreviated description of the implemented enhancement projects (detailed

descriptions are found in memos prepared by Jean Ferreira dated August 1995 and one
undated memo [presumably dated Spring 1997]):

Connect Lagoon to North Pond (1993 and repair 1997):

The goal of this work was to increase tidal prism in the marsh and to increase circulation
and waterfowl habitat in North Pond. This was done by constructing a new channel
(Elements A1 and A3) from the North Marsh Levee to North Pond. Six 4.0-foot diameter
culverts (set below sea level) and two 1-foot diameter culverts (set above sea level), each
with manual slide gate, were installed at the new channel's inlet (Element A2). A levee
was constructed to divide the new connecting channel on the west from North Marsh to
the east (Element A2). The operation of the six 4.0 foot culverts included keeping them
open from early fall through the winter and into early summer. When the sandbar at the
lagoon mouth was closed, the gates would be manually shut allowing only overflow
through the higher 1.0-foot culverts. The dividing levee, constructed with dredge spoils
from the marsh, breached between 1993 and 1996 and was repaired in 1997. It was found
breached again in early summer of 2000.

Increase the size of Breaches in levee in the Butano Marshes (1993):

The goal of this work was to increase tidal prism and water circulation between the East,
Middle and North Butano Marshes and to improve flood conveyance from Butano Creek
through the Butano Marshes.

The openings between the levees in the Butano Marshes were expanded in the following
way:

Element C1: An existing gap between North Butano Marsh and Butano Creek was
widened to 50 feet.

Element C2: The levee between Middle and East (south) Butano Marshes was breached
with a 100-foot gap and a 125-foot long channel to connect channels on either side of the
levee.

Hydrology / Geomorphology / Restoration / Water Resources / Construction Planning

& Supervision
 Swanson Hydrology & Geomorphology
Page 3
Element C3: The levee between Middle and North Butano Marshes was breached 100-
feet wide and a 125-foot long channel was constructed to connect the existing channel on
either side of the levee.

Element C4: The levee was removed on the west bank of Butano Creek from the "Triple
Junction" (the point where three levees meet on the west side of Butano Creek between
the Middle and East Butano Marshes) to a point downstream 250 feet from the Triple
Junction.

Remove Delta Marsh Levee (1997)

Approximately 1,500 linear feet (the exact length should be measured off new aerials) of
levee was removed from the north and western perimeter of East Delta Marsh in 1997.
The purpose of this work was to improve hydrologic function of the East Delta Marsh,
improve visual appearance and to improve the flood conveyance through the Delta Marsh
from overflow of Butano Creek.

Key Issues to be addressed.

The recommendations presented below are designed to update technical information, fix
any problems and perhaps move forward with new enhancement projects. The 1990
Enhancement Plan was only partially implemented due to funding constraints; the key
element not implemented was to excavate the east bank of Butano Creek, restore it to
marsh/floodplain and to raise the agricultural land to the east.

New conditions require that CDPR review and perhaps revise their goals and objectives
for the Marsh prior to developing and analyzing management measures and alternatives.
It has become apparent that information in the Plan has become dated and that the
regulations surrounding specific special status species, notably steelhead trout and red-
legged frog, have changed. Personnel and Management staff at CDPR have changed as
well. In addition, local agencies are preparing a Watershed Assessment of geomorphic
conditions, habitat quality and watershed factors that affect marsh habitat quality.

To target key topics, the areas will be discussed by geographic area as identified in Figure
1 of the 1990 Enhancement Plan.

BUTANO CREEK

The upper reaches of Butano Creek has steadily aggraded with sediment since the early
1960s. It appears that at least 8 feet has filled a 3,200-foot long reach from a point 1,200
feet above the Pescadero Creek Road Bridge to a point 2,000 feet downstream. This has
resulted in a loss of flood capacity and has been a source of controversy and litigation for
over 20 years. The reasons for aggradation appear to be a combination of factors. These
include: disruption of sediment transport continuity in the channel caused by the
historical channelization and levee construction along the creek and in the marsh,
construction of the Pescadero Creek Road and bridge, maintenance of open areas on the
east side of the creek in agricultural lands and excessive erosion and sediment delivery
from the watershed caused by land disturbance, channel incision and large storm events
Hydrology / Geomorphology / Restoration / Water Resources / Construction Planning
& Supervision
 Swanson Hydrology & Geomorphology
Page 4
(e.g. 1982-83; 1995 and 1998). Based upon available data, it is estimated that over 20,000
yards of sand has been deposited in Butano Creek since 1960.

The primary cause of aggradation appears to be loss of sediment transport capacity at the
head of the valley 1,200 feet upstream of the bridge where significant overflow to the east
removes hydraulic force from the channel while sand bedload moving in the channel
remains. This process is self-reinforcing in that as more sand is deposited in the channel,
more flow goes overbank resulting in greater loss of hydraulic force and in turn more
sand deposition. The levees along lower Butano Creek prevent overbank flow from re-
entering the channel during flood recession when normal channel scour usually occurs.
Thus, the channel is no longer maintained by scour when overbank floodwaters recede.
The overflow on the east bank usually causes nuisance flooding every year (over 25 days
of flow over Pescadero Road occurred in the 1999-2000 winter) and significant flooding
through private lands during major storms (e.g. February 1998, about a 25-year flood
event).

The bridge structure also blocks overbank flow downstream of the bridge to the large
conveyance areas in the Butano Marshes. Topographic surveys conducted by Swanson
Hydrology and Geomorphology in 1999 show that the Butano Creek channel downstream
of Pescadero Creek Road is several feet higher than the East Butano Creek Marshes to
the west; undoubtedly the creek would be flowing in the Butano Marshes were it not for
the blockage of Pescadero Creek Road.

Observations of Butano Creek during summer low flow indicates that most if not all
summer flows spill out of the Butano Creek channel and into the adjacent marshes. A
2,000-foot long blockage of sediment, willow and tules, some possibly related to beaver
dams, occurs 900 feet below the Pescadero Creek Bridge.

The constructed components of the 1990 Enhancement Plan involved breaching sections
of levees connecting the Butano Marshes. This would allow for greater flood conveyance
through the marshes if it were not for the blocking effect of the bridge.

In terms of ecological management, blockage of Butano Creek may have three negative
effects:

1) Down migrating young steelhead may become stranded or may be subject to greater
predation by waterfowl when swept into open marsh areas on Butano Creek as a
result of blockage by sediment and vegetation.

2) Smith and Reis (1997) report that any management action that increases perennial
freshwater marsh will favor successful bullfrog breeding, a condition that the
plugged Butano Creek channel has certainly created in adjacent Butano Marshes
and East Delta Marsh. Bullfrogs, a non-native species, prey on the federally listed
red-legged frog.

3) The lack of flushing flood flows directed into the Butano Marshes has eliminated
natural deltaic conditions and the associated dynamic landforms (i.e. deltaic lobes,
meandering channels, natural levees, oxbows, crevass splays). The variety of
Hydrology / Geomorphology / Restoration / Water Resources / Construction Planning
& Supervision
 Swanson Hydrology & Geomorphology
Page 5
landforms in a deltaic system creates biotic diversity by diversifying the
topographic relief and the relationship between land and water. This in turn
presents diverse conditions for native wetland and riparian vegetation and water
depths in channels and emergent marsh. The lack of dynamic geomorphic
processes, and perhaps the breaching of levees around the Butano Marshes in
1993 allowing more freshwater input, has led to the uniform cover of tule and
cattail found today and the apparently low but unquantified biotic diversity.

A study of the Pescadero Creek Road Bridge in 1999 (completed by Swanson Hydrology
for San Mateo County) found that simple modification of the bridge reduced nuisance
flooding, but achieved no greater than 2 to 5 year flood protection for adjacent private
land. A more comprehensive project, involving expansion of the bridge, dredging Butano
Creek and raising the east bank of the stream may achieve 10-year or great protection for
adjacent lands. However, potential impacts to the floodplain caused by new berms may
affect floods greater than 10-year and may be difficult to mitigate. Other projects could
include relocating the creek to either Butano Marshes or along the eastern side of the
existing creek. Any of the larger scale plans will involve modification of the bridge and
close cooperation with San Mateo County, landowners, and regulatory agencies. The
presence of four special status species will require additional effort in planning
construction and expenditure. In addition, there has been documentation of contaminated
soils in the area from past pesticide use. It is unknown whether permitting would be
successful.

It is apparent that actions by CDPR alone cannot solve the adjacent landowners drainage
problems along Butano Creek. Whether benefits from an ecological standpoint can be
achieved requires further examination, especially with respect to the management of
endangered species during and after construction. More planning is needed to assess
whether dredging and other drainage projects might require future maintenance
(sediment, vegetation or beaver dam removal) and what the impacts and costs might be.

Recommendations

1) Investigate whether modifications of Butano Creek could achieve CDPR goals for
ecological management, especially reducing freshwater habitats that favor
bullfrogs, downstream migration of steelhead trout and restoration of deltaic
function to the Butano Marshes. The hydraulic model prepared for the San Mateo
County bridge study could be modified to simulate the function of improvements.
The study should be coordinated with other involved agencies (i.e. San Mateo
County).

2) Re-survey 1987 channel cross sections to determine changes over past 12 years; map
vegetation cover to assess flood plain and marsh vegetation changes and hydraulic
changes.

3) Investigate the benefits and impacts of creating a functional channel flood

plain systems and expanding the riparian corridor from CDPR lands
upstream to the head of the valley?

Hydrology / Geomorphology / Restoration / Water Resources / Construction Planning

& Supervision
 Swanson Hydrology & Geomorphology
Page 6
Important questions:

What would the impact of increasing flood flows and sediment deposition to East
Butano Marshes if the Pescadero Creek Road Bridge were modified?
Has aggradation of Butano Creek created more perennial wetland that favors successful
bullfrog breeding and therefore predation on red-legged frog?

What would the impacts of construction activity be on endangered species and

habitats? How might these be addressed?

What is the risk of failure if dredged Butano Creek refills with sediment?

What is the impact of the existing obstruction in Butano Creek on steelhead

trout down migrants and predation?

BUTANO MARSHES

The Butano Marshes (East, Middle and North) are bounded by reclamation levees. As
described above some of these levees were breached in 1993. Smith and Reis (1997)
report that the effect has been to freshen them in the winter and early spring and make
them saltier in late spring and summer. This change in salinity regime does not favor red-
legged frog or San Francisco Garter Snake habitats, although it is unknown what pre-
1993 habitat conditions were. The levee breaches have apparently increased bullfrog
circulation between Butano Creek and the Butano Marshes.

As noted above, the Butano Marshes have become covered with dense stands of tule and
bullrush compared with conditions in the late 1980s. The reason may be the greater
freshwater circulation made available by breaching the levees in 1993 and through the
overflow from a clogged Butano Creek.

Recommendations

1) Investigate the impact of the 1993 levee breaching on red-legged frog

populations by conducting a new survey and assessment per Smith and
Reis (1997).
2) Investigate the vegetative changes in the Butano Marshes over the past 12
years and estimate the net ecological changes.
3) Investigate the potential to redirect Butano Creek into the East Butano Marsh.

EAST DELTA MARSH

A 1,200-foot long section of levee was removed from East Delta Marsh and along the
east bank of Butano Creek in 1997 to achieve similar goals as levee removal in the
Butano Marshes. Adult red-legged frogs and bullfrogs were found in Delta Marsh in 1996
by Smith and Reis (1997), who as a result, made specific recommendations for the levee

Hydrology / Geomorphology / Restoration / Water Resources / Construction Planning

& Supervision
 Swanson Hydrology & Geomorphology
Page 7
removal to protect and enhance red-legged from habitat. It is unknown whether these
recommendations were followed and what populations are now.

The land upstream of East Delta Marsh and east of Butano Creek has changed
dramatically since the late 1980s. In 1987, the area was cultivated in artichokes nearly up
to the east bank of Butano Creek. Much of the land was acquired by CDPR, but was
leased to a commercial willow growing operation for several years. The operation utilized
non-reproducing, non-native species. When CDPR ended the lease, the furrows and
willows remained and other wetland vegetation has since colonized the area. The area
appears to be becoming a riparian forest. The original enhancement plan envisioned that
the area between East Delta Marsh and the Muzzi Parcels (now Cook parcels) on
Pescadero Creek Road would be excavated to an elevation of about 5.0 feet and a new
Butano Creek channel would be constructed. The spoils would be used to raise the private
agricultural lands to the east and southeast. The intent was to create a floodway and a
"functional" Butano Creek channel without impacting endangered species (mainly San
Francisco Garter Snake and now also red-legged frog). This portion of the plan was not
implemented in part because the Muzzi parcels werent purchased.

Recommendations

1) Conduct biological survey for red-legged frog in Delta Marsh.

2) Investigate the viability of carrying out the 1990 Enhancement Plan for Butano
Creek (i.e. lowering the east bank and constructing a new Butano creek
channel) as an alternative to increasing flows to the Butano Marshes by
modifying the Pescadero Creek Road Bridge.

NORTH POND AND NORTH MARSH

Prior to the 1990 Enhancement Plan, North Pond was hydrologicaly isolated from North
Marsh and Pescadero Creek Lagoon. To improve tidal circulation to North Pond, the
culverts connecting the lagoon to North Marsh were replaced; a channel was excavated
along the west edge of North Marsh to North Pond. The project included physical
manipulation of the culverts by CDPR staff closing them to enable the barrier beach to
close the lagoon mouth in late spring or summer, and opening them to tidal circulation
when the lagoon mouth is open. Park Ranger Michael Grant operated the gates up
through 2000, although operation of the gates is difficult due to corrosion of the gear
mechanisms. A levee was constructed along the east side of the new tidal channel in order
to separate salt water from the freshwater habitat of North Marsh, where significant red-
legged frog populations and abundant evidence of breeding have been found (Smith and
Reis, 1997).

As noted above, inspection of North Marsh / North Pond system in summer 2000 found
that the separating levee had breached again (similar to 1997) allowing salt water into
North Marsh. This may have had negative impacts on red-legged frog and tidewater goby
habitats although this has not been studied. Smith and Reis (1997) found that Tidewater
Hydrology / Geomorphology / Restoration / Water Resources / Construction Planning
& Supervision
 Swanson Hydrology & Geomorphology
Page 8
Goby habitat had decreased significantly after construction due to increased salinity and
stronger currents.

Restoring tidal circulation to North Pond increased the tidal prism in the Marsh and the
scouring force of ebb tide outflow that opens the barrier beach at the lagoon and creek
mouth. As anticipated in proposed slide gate closure provisions in the plan, this may
delay seasonal closure of the lagoon in early summer and reduce the period of high water
(3-4 feet higher) in the lagoon. High water in the lagoon expands aquatic and freshwater
habitat by increasing depth and inundation area; it is unknown whether this increases or
does not affect bullfrog-breeding habitat.

Recommendations

1) Conduct red-legged frog and water quality survey per methods of Smith and Reis
(1997).

2) Develop a revised version of the water quality strategy to manage the habitat.
Determine the viability of operating the current slide gates and whether the
personnel resources are available. Determine if a self operating system is feasible.

3) Investigate the potential hydrological and biological ramifications of the breached

dividing levee and the eroding levee containing the slide gates. Determine the
possible long-term effects of not repairing the levee structures. Update
hydrological vision for the marsh ecosystem to determine a long-term plan for
these structures.

PESCADERO CREEK AND LAGOON

No specific enhancement work was completed on Pescadero Creek. However, there are
some significant opportunities for enhancement as well as issues related to erosion and
flooding.

The main issues are related to erosion under a levee section at the southeast corner of
CDPR's property near the end of Water Lane. Bank erosion has progressed undermining a
section of levee where Pescadero Creek turns 90-degrees northward. Besides this issue,
there are some opportunities to expand riparian habitat by setting back or removing
levees and lowering terraces surfaces.

The Pescadero Creek Lagoon has been the subject of several studies spanning the past 20
years. In general, it is believed that seasonal closure of the lagoon by closing the sandbar
creates deeper and more extensive aquatic habitat and good conditions in late spring,
summer and fall habitat for steelhead and Tidewater Goby.

One aspect that has not been considered is the effect of excessive nutrient loading on
primary productivity, dissolved oxygen levels, development of anoxic conditions and
H2S gas release. This may be an important process that apparently has not been
addressed in any detail, although high nutrient levels in Pescadero Creek are well known.
The effect of excessive nutrients may explain recent fish kills in the lagoon.
Hydrology / Geomorphology / Restoration / Water Resources / Construction Planning
& Supervision
 Swanson Hydrology & Geomorphology
Page 9

Recommendations

1) Investigate bank protection options for the 90-degree bend on Pescadero Creek with
consideration of appropriate habitat characteristics for riparian vegetation,
steelhead trout and red-legged frog. Consider use of larger redwood logs and
bioengineering techniques. Assess geomorphic and hydraulic conditions.

2) Investigate projects that would expand riparian habitat along Pescadero Creek
including setting back levees east of Water Lane and removing levee segments
just east of Round Hill. Each of these options should be developed with a
hydraulic model in order to test for potential flooding and sediment impacts.

3) Conduct data collection and analysis to address water quality impacts of excessive
nutrients on biogeochemical processes, dissolved oxygen and H2S gas
development in sediments and release to the water column. Revise lagoon
management aspects based upon consideration of physical habitat and
biogeochemical processes. Revise operation of North Marsh slide gates
accordingly.

References

Smith J.J. and Dawn K. Reis, 1997: Pescadero Marsh Natural Preserve Salinity,
Tidewater Goby, and Red-Legged Frog monitoring for 1995-96; unpublished
report presented to California Department of Parks and Recreation (3790-301-
722(7)) 16 pages plus maps and tables.

Swanson Hydrology and Geomorphology, 1999: Hydraulic Study of the Pescadero Creek
Road crossing over Butano Creek, unpublished report to the San Mateo County
Public Works Department, 78 pages plus figures and tables.

Williams, J. G, 1990: Pescadero Marsh Natural Preserve Hydrological Enhancement

Plan; unpublished report by Philip Williams & Associates to California
Department of Parks and Recreation, 64 pages plus appendices.

Hydrology / Geomorphology / Restoration / Water Resources / Construction Planning

& Supervision
 Swanson Hydrology & Geomorphology
Page 10

SCOPE OF WORK FOR AN UPDATED ENHANCEMENT PLAN

Task 1: Refine Enhancement Plan Goals and Objectives

Revise the goals (what the plan should accomplish) and objectives (what study and
research should produce) of the updated plan. Use these as a guide for new data
collection and analysis and for formulating revised management measures.

Task 2: Update Scientific Database

Task 2a: Update Biotic Information

Biotic information should be updated to document vegetation and habitat changes in the
marsh and in the creek corridors. A key focus area should be red-legged frog surveys of
North Marsh, Butano Marshes and Delta and East Delta Marshes. Vegetation changes
should be completed by a comparison of earlier maps of vegetation communities with a
current map. Causes and implications of vegetative changes should be identified. Wildlife
lists should be updated and a comparison of conditions in the late 1980s to today's
conditions should be made.

Task 2b: Update Hydrologic and Geomorphic Information

An assessment of geomorphic and hydrologic changes since the late 1980s should be
completed incorporating the effects of the enhancement projects completed in 1993 and
1997, the effects of large floods in the 1990s, recent studies and new field data.

The topographic data should be updated at select locations in the marsh. This would be
especially informative on Lower Butano Creek to determine how much aggradation has
occurred since the late 1990s. Hydrologic changes associated with the constructed
enhancement projects should also be documented. Use of continuous water level
recorders and water quality gages are recommended to evaluate circulation, and
biogeochemical processes.

A hydraulic model should be constructed to assess sediment transport and flooding

dynamics on Pescadero and Butano Creeks. This would enable estimation of the effects
of various proposals such as improving the Pescadero Creek Road Bridge, lowering the
east bank of Butano Creek or setting back levees on Pescadero Creek. The model could
be used to evaluate the effects of dredging Butano Creek and the need for long-term
maintenance measures.

Task 2c: Update Regulatory Issues

Hydrology / Geomorphology / Restoration / Water Resources / Construction Planning

& Supervision
 Swanson Hydrology & Geomorphology
Page 11
Regulatory issues should be updated in order to determine permitting and mitigation
issues. The major concerns would be endangered species management and coastal
development permitting.

Task 3: Identify Opportunities and Constraints

All opportunities and constraints relevant to implementing enhancement projects and

management of the Marsh should be identified with respect to funding and personnel
resources, regulatory issues, physical, biological and political realities. These may
include potential for collaborative funding with agencies such as California Department
of Fish and Game and/or local and federal agencies. Personnel commitments to operating
slide gates and other devices should be realistically assessed.

Task 4: Develop Alternatives

A range of alternative management plans should be developed given the set of goals and
objectives, new scientific and planning data and the opportunities and constraints. The
alternatives could be different combinations of project elements but there should be an
assessment of benefits and impacts combined and cumulatively. Cost estimates for
various management measures should be developed.

Task 5: Identify and Document Preferred Alternative

An analysis of alternatives should yield a preferred plan. The details of the preferred plan
should be developed including an implementation plan. Details related to permitting,
construction, maintenance and monitoring should also be devised.

Hydrology / Geomorphology / Restoration / Water Resources / Construction Planning

& Supervision